MakeDOCK 2.0, modified by J.Irwin and M.Mysinger. Previous versions by D.M.Lorber, B.Q.Wei, A.N.Kirschner, and N.Huang Using scripts in /raid5/people/mysinger/xyz/dockenv. Creating binding-site residue list Creating molecular surface real 0m2.393s user 0m0.305s sys 0m0.218s Creating sphgen spheres Enter name of sphere cluster file: Enter cluster number to process (<0 = all): Generate surfaces as well as pdb files (/Y)? Enter name for output PDB file name: Cluster 0:1305 spheres. 180. 180. 180. 180. 180. 180. 180. 180. 180. 180. 182. 182. 182. 182. 182. 182. 183. 183. 183. 183. 183. 183. 183. 183. 183. 183. 183. 183. 183. 183. 183. 183. 183. 183. 199. 199. 199. 199. 199. 199. 209. 209. 209. 209. 209. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 212. 212. 212. 212. 212. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 216. 219. 221. 221. 221. 221. 221. 221. 221. 222. 222. 222. 222. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 224. 226. 226. 228. 228. 228. 228. 228. 229. 229. 230. 230. 230. 230. 230. 230. 230. 230. 231. 231. 231. 231. 231. 231. 243. 244. 244. 244. 244. 244. 244. 244. 244. 244. 244. 244. 244. 244. 244. 342. 342. 342. 342. 345. 345. 345. 345. 345. 345. 345. 345. 345. 345. 345. 345. 345. 345. 345. 345. 352. 352. 352. 353. 355. 355. 355. 355. 355. 355. 355. 355. 355. 355. 356. 356. 356. 360. 362. 362. 362. 362. 362. 362. 362. 362. 363. 363. 363. 363. 364. 364. 364. 364. 364. 364. 364. 364. 364. 364. 364. 364. 364. 364. 364. 364. 364. 364. 366. 366. 369. 369. 369. 369. 369. 369. 369. 371. 371. 371. 371. 371. 371. 372. 372. 372. 372. 373. 373. 375. 375. 375. 375. 375. 375. 375. 375. 375. 375. 375. 375. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 376. 377. 377. 377. 378. 378. 378. 378. 378. 378. 378. 378. 378. 378. 378. 378. 378. 378. 378. 378. 378. 378. 378. 378. 378. 378. 380. 380. 380. 380. 380. 380. 380. 380. 380. 380. 381. 385. 385. 386. 386. 386. 386. 386. 386. 386. 388. 388. 388. 388. 388. 388. 388. 388. 388. 388. 388. 388. 388. 388. 388. 388. 388. 388. 388. 388. 388. 388. 388. 388. 388. 388. 388. 388. 388. 388. 388. 389. 389. 391. 392. 392. 392. 392. 392. 392. 392. 392. 392. 392. 392. 392. 392. 392. 392. 392. 392. 392. 394. 394. 394. 394. 394. 394. 394. 394. 400. 401. 401. 402. 402. 402. 403. 403. 403. 403. 403. 403. 403. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 407. 407. 407. 407. 407. 407. 407. 407. 407. 407. 407. 407. 407. 407. 407. 414. 414. 414. 414. 414. 414. 415. 446. 446. 446. 446. 446. 446. 449. 449. 449. 449. 449. 449. 450. 450. 450. 450. 450. 451. 451. 451. 451. 451. 451. 593. 593. 593. 602. 604. 604. 604. 604. 604. 604. 604. 604. 605. 605. 605. 606. 611. 611. 611. 613. 613. 618. 619. 619. 619. 619. 619. 619. 619. 619. 619. 619. 619. 619. 619. 619. 619. 619. 619. 619. 620. 620. 620. 620. 620. 620. 620. 620. 620. 620. 620. 620. 620. 620. 620. 620. 620. 620. 620. 620. 620. 620. 620. 620. 620. 620. 621. 621. 621. 621. 626. 626. 626. 626. 626. 626. 626. 626. 626. 626. 626. 626. 626. 626. 626. 626. 626. 626. 626. 626. 626. 626. 626. 626. 626. 626. 626. 626. 626. 626. 626. 630. 634. 634. 634. 634. 634. 634. 634. 634. 634. 634. 634. 634. 634. 634. 634. 634. 634. 634. 640. 640. 640. 640. 641. 642. 642. 642. 642. 642. 642. 642. 642. 642. 642. 642. 642. 642. 642. 657. 663. 663. 664. 664. 664. 664. 664. 664. 664. 664. 664. 664. 665. 667. 667. 667. 667. 667. 669. 669. 669. 670. 670. 670. 670. 670. 670. 670. 670. 670. 673. 821. 824. 824. 824. 824. 824. 826. 826. 827. 827. 827. 827. 827. 827. 827. 827. 827. 827. 827. 827. 827. 827. 827. 827. 827. 827. 828. 828. 828. 828. 828. 828. 828. 828. 828. 828. 828. 828. 828. 829. 829. 829. 829. 829. 829. 829. 829. 829. 829. 829. 830. 830. 830. 831. 831. 831. 831. 831. 831. 831. 831. 831. 831. 831. 831. 831. 831. 831. 831. 831. 831. 831. 831. 831. 831. 831. 831. 833. 833. 833. 833. 833. 834. 834. 834. 834. 834. 834. 842. 842. 842. 842. 842. 845. 845. 845. 845. 845. 845. 845. 845. 845. 845. 845. 845. 845. 845. 846. 846. 846. 846. 846. 846. 846. 846. 846. 846. 846. 846. 846. 846. 846. 846. 846. 846. 846. 846. 846. 846. 846. 930. 930. 938. 938. 938. 938. 938. 938. 940. 941. 941. 941. 941. 941. 941. 941. 941. 941. 941. 941. 957. 957. 957. 957. 957. 957. 957. 961. 967. 967. 967. 967. 968. 968. 968. 968. 968. 968. 968. 968. 968. 968. 968. 968. 968. 968. 968. 968. 968. 968. 968. 968. 968. 970. 970. 970. 970. 970. 973. 973. 973. 973. 973. 973. 973. 973. 973. 973. 973. 973. 973. 973. 973. 973. 973. 973. 974. 979. 979. 979. 979. 979. 979. 979. 980. 980. 980. 980. 980. 980. 980. 980. 980. 980. 980. 980. 980. 981. 981. 981. 981. 981. 981. 981. 981. 981. 981. 981. 981. 981. 981. 981. 981. 981. 981. 981. 981. 981. 981. 981. 981. 981. 981. 981. 981. 981. 981. 981. 981. 981. 982. 984. 984. 984. 985. 986. 986. 986. 986. 986. 986. 986. 986. 988. 988. 988. 988. 989. 989. 989. 989.1001.1001.1002.1002.1002.1002.1002.1002.1002.1002.1002.1002.1002.1002.1002.1013.1013.1013.1013.1016.1016.1016.1016.1016.1016.1018.1019.1019.1019.1019.1019.1020.1020.1020.1124.1124.1124.1127.1127.1127.1127.1127.1127.1127.1127.1129.1129.1129.1129.1129.1130.1130.1130.1130.1130.1131.1131.1131.1132.1132.1132.1132.1132.1133.1133.1133.1133.1133.1133.1133.1133.1133.1133.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1135.1135.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1138.1138.1138.1138.1139.1143.1143.1143.1144.1144.1144.1144.1144.1144.1144.1146.1146.1146.1146.1146.1146.1146.1146.1146.1146.1146.1146.1146.1146.1146.1146.1146.1146.1146.1146.1146.1146.1146.1146.1146.1146.1146.1146.1146.1146.1146.1146.1147.1147.1149.1150.1150.1150.1150.1150.1150.1150.1150.1150.1150.1150.1150.1150.1150.1150.1150.1152.1152.1152.1153.1153.1153.1153.1172.1172.1172.1172.1172.1360.1360.1360.1360.1360.1360.1360.1360.1360.1360.1360.1362.1362.1362.1362.1362.1362.1362.1362.1363.1363.1364.1369.1369.1369.1369.1371.1371.1371.1374.1376.1376.1376.1376.1376.1376.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1378.1378.1378.1378.1378.1378.1378.1378.1378.1378.1378.1378.1378.1378.1378.1378.1378.1378.1378.1378.1378.1378.1378.1378.1378.1378.1378.1378.1378.1378.1378.1379.1379.1379.1379.1384.1384.1384.1384.1384.1384.1384.1384.1384.1384.1384.1384.1384.1384.1384.1384.1384.1384.1384.1384.1384.1384.1384.1384.1384.1384.1384.1384.1384.1384.1384.1384.1384.1384.1384.1384.1384.1384.1384.1384.1384.1384.1384.1384.1384.1384.1388.1391.1391.1391.1398.1398.1398.1398.1399.1400.1400.1400.1400.1400.1400.1400.1400.1400.1400.1400.1400.1400.1400.FORTRAN STOP Converting ligand atoms to spheres Enter name of sphere cluster file: Enter cluster number to process (<0 = all): Generate surfaces as well as pdb files (/Y)? Enter name for output PDB file name: Cluster 1: 33 spheres. 1. 2. 3. 4. 5. 6. 7. 8. 9. 10. 11. 12. 13. 14. 15. 16. 17. 18. 19. 20. 21. 22. 23. 24. 25. 26. 27. 28. 29. 30. 31. 32. 33.FORTRAN STOP Adding essential hydrogens to receptor Adding all-atom hydrogens... Working on structure 1 Pre-treating metals... Done treating metals Adding hydrogens... Treating metals... Creating di-sulfur bonds... Detecting missing residue atoms... Finding het groups... Coloring atoms by element (green carbons in hets)... Running ProtAssign... using exhaustive mode will sample waters done with preparation Writing to file... DONE. Output file: rec.mae Removing non-polar hydrogens... Renaming polar hydrogens... Generating matching spheres for delphi Enter name of sphere cluster file: Enter cluster number to process (<0 = all): Generate surfaces as well as pdb files (/Y)? Enter name for output PDB file name: Cluster 1: 120 spheres. 9001.9002.9003.9004.9005.9006.9007.9008.9009.9010.9011.9012.9013.9014.9015.9016.9017.9018.9019.9020.9021.9022.9023.9024.9025.9026.9027.9028.9029.9030.9031.9032.9033.9034.9035.9036.9037.9038.9039.9040.9041.9042.9043.9044.9045.9046.9047.9048.9049.9050.9051.9052.9053.9054.9055.9056.9057.9058.9059.9060.9061.9062.9063.9064.9065.9066.9067.9068.9069.9070.9071.9072.9073.9074.9075.9076.9077.9078.9079.9080.9081.9082.9083.9084.9085.9086.9087.9088.9089.9090.9091.9092.9093.9094.9095.9096.9097.9098.9099.9100.9101.9102.9103.9104.9105.9106.9107.9108.9109.9110.9111.9112.9113.9114.9115.9116.9117.9118.9119.9120.FORTRAN STOP Generating faster matching2 spheres for docking Enter name of sphere cluster file: Enter cluster number to process (<0 = all): Generate surfaces as well as pdb files (/Y)? Enter name for output PDB file name: Cluster 1: 45 spheres. 9001.9002.9003.9004.9005.9006.9007.9008.9009.9010.9011.9012.9013.9014.9015.9016.9017.9018.9019.9020.9021.9022.9023.9024.9025.9026.9027.9028.9029.9030.9031.9032.9033.9034.9035.9036.9037.9038.9039.9040.9041.9042.9043.9044.9045.FORTRAN STOP Coloring matching spheres Generating slower matching3 spheres for docking Enter name of sphere cluster file: Enter cluster number to process (<0 = all): Generate surfaces as well as pdb files (/Y)? Enter name for output PDB file name: Cluster 1: 60 spheres. 9001.9002.9003.9004.9005.9006.9007.9008.9009.9010.9011.9012.9013.9014.9015.9016.9017.9018.9019.9020.9021.9022.9023.9024.9025.9026.9027.9028.9029.9030.9031.9032.9033.9034.9035.9036.9037.9038.9039.9040.9041.9042.9043.9044.9045.9046.9047.9048.9049.9050.9051.9052.9053.9054.9055.9056.9057.9058.9059.9060.FORTRAN STOP Coloring matching spheres Adding spheres to electrostatic grid we had to cook * HD2* Creating DelPhi electrostatic grid real 0m56.941s user 0m52.543s sys 0m2.450s Adding spheres to tarted electrostatic grid we had to cook * HD2* Creating DelPhi electrostatic grid real 0m59.239s user 0m54.745s sys 0m2.261s Creating box around spheres we had to cook * HD2* Creating chemgrid maps real 1m35.845s user 1m34.297s sys 0m0.924s Atomic solvent excluded volume calculations underway FORTRAN STOP real 29m15.263s user 29m14.478s sys 0m0.204s Checking for WARNINGS in OUTPARM. Checking for WARNINGS in delphi.log. !!! WARNING: ASH 25 has a net charge of -0.3190 !!! WARNING: ASH 25 has a net charge of -0.3190 !!! WARNING: ASH 25 has a net charge of -0.3190 End of MakeDOCK sphere and grid generation.